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- PDB-6ym1: Mycobacterium tuberculosis FtsZ in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 6ym1
TitleMycobacterium tuberculosis FtsZ in complex with GDP
ComponentsCell division protein FtsZ
KeywordsANTIBIOTIC / Cell division Protein
Function / homology
Function and homology information


division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal ...Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Cell division protein FtsZ
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAlnami, A.T. / Norton, R.S. / Pena, H.P. / Haider, M. / kozielski, F.
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Conformational Flexibility of A Highly Conserved Helix Controls Cryptic Pocket Formation in FtsZ.
Authors: Alnami, A. / Norton, R.S. / Pena, H.P. / Haider, S. / Kozielski, F.
History
DepositionApr 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _struct.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein FtsZ
B: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4113
Polymers63,9682
Non-polymers4431
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-10 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.542, 88.542, 178.116
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Cell division protein FtsZ


Mass: 31984.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Gene: ftsZ, MT2209 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WN94
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 5.6
Details: 27.5% PEG4000, 0.4 M ammonium acetate and 0.1 M Na citrate, soaked with 5 mM GDP for 2 hr

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Data collection

DiffractionMean temperature: 86 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.7→76.68 Å / Num. obs: 86575 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 30.14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Net I/σ(I): 9.5
Reflection shellResolution: 1.7→1.79 Å / Num. unique obs: 12573 / CC1/2: 0.668

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rq7

1rq7


Resolution: 1.7→76.68 Å / SU ML: 0.1911 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3816
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2077 4299 4.99 %
Rwork0.1753 81898 -
obs0.1769 86197 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.95 Å2
Refinement stepCycle: LAST / Resolution: 1.7→76.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4206 0 0 326 4532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124361
X-RAY DIFFRACTIONf_angle_d1.22975949
X-RAY DIFFRACTIONf_chiral_restr0.0832734
X-RAY DIFFRACTIONf_plane_restr0.007789
X-RAY DIFFRACTIONf_dihedral_angle_d5.97593513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.30921360.28112653X-RAY DIFFRACTION98.73
1.72-1.740.30241610.28682693X-RAY DIFFRACTION98.38
1.74-1.760.26721450.26722680X-RAY DIFFRACTION98.5
1.76-1.780.33641170.26982733X-RAY DIFFRACTION99.06
1.78-1.810.27891300.24982781X-RAY DIFFRACTION99.39
1.81-1.830.28271520.24322633X-RAY DIFFRACTION99.18
1.83-1.860.25431680.22872691X-RAY DIFFRACTION99.51
1.86-1.890.26811410.22482767X-RAY DIFFRACTION99.52
1.89-1.910.25411290.21552725X-RAY DIFFRACTION99.83
1.91-1.950.24061530.21052702X-RAY DIFFRACTION99.76
1.95-1.980.22931380.19742742X-RAY DIFFRACTION99.79
1.98-2.020.20911590.19562739X-RAY DIFFRACTION99.86
2.02-2.050.25311240.19392760X-RAY DIFFRACTION99.93
2.05-2.10.21951550.19092725X-RAY DIFFRACTION100
2.1-2.140.19941760.18672681X-RAY DIFFRACTION99.9
2.14-2.190.20711410.17992745X-RAY DIFFRACTION99.9
2.19-2.250.23181430.18462715X-RAY DIFFRACTION99.76
2.25-2.310.20831270.17762758X-RAY DIFFRACTION99.83
2.31-2.380.22461360.17742747X-RAY DIFFRACTION99.79
2.38-2.450.19731520.17842736X-RAY DIFFRACTION99.76
2.45-2.540.22841180.18462761X-RAY DIFFRACTION99.76
2.54-2.640.21961360.18582740X-RAY DIFFRACTION99.9
2.64-2.760.20271680.18482715X-RAY DIFFRACTION99.93
2.76-2.910.22221390.18452722X-RAY DIFFRACTION99.9
2.91-3.090.23751750.18722711X-RAY DIFFRACTION100
3.09-3.330.21551620.17442743X-RAY DIFFRACTION100
3.33-3.660.18831500.15762755X-RAY DIFFRACTION100
3.66-4.190.18611410.15172751X-RAY DIFFRACTION100
4.19-5.280.16381030.1392792X-RAY DIFFRACTION100
5.28-76.680.17111240.16632802X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: 37.7374043009 Å / Origin y: -23.7403724973 Å / Origin z: 11.5118581844 Å
111213212223313233
T0.216792169051 Å20.00345713873454 Å2-0.0154837337565 Å2-0.268343708839 Å20.0112264250785 Å2--0.224060607224 Å2
L0.5966178255 °2-0.417715194423 °20.109423761444 °2-2.0859739712 °2-0.283335909739 °2--0.461054495784 °2
S-0.0546041615268 Å °0.0619831007607 Å °0.0249791066929 Å °0.158878539563 Å °0.0727960626279 Å °-0.00971281211662 Å °-0.114218115341 Å °0.0439532315689 Å °-0.0186029071767 Å °
Refinement TLS groupSelection details: all

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